The safest textured background palette entries are 176-207. It's important to ensure that every color from the 176-207 range is used in your tileset image, otherwise JCS will try to be helpful and, during tileset compilation, regardless of settings, replace the unused entries with colors it thinks are more important (mostly for better 8-bit color ambient lighting). This won't make a difference in 16-bit color mode because it uses smart gradients, but 8-bit mode just assumes colors in the background range create valid transitions, and if, thanks to JCS, they don't, well, results can be terrible.
Or that's what I assume because I never actually looked into that part of code. Sounds like a good enough explanation though.